Methylation Glioblastoma

Methylation Glioblastoma

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Gliomas are the most common neoplasm of the central nervous system, they originate from glia cells, which are supporting cells of the brain and spinal cord.

Gliomas are divided into three groups depending on the origin of the malignancy. Astrocytoma is the most common type of gliomas affecting both children and adults, comprising around 30% of all diagnosed brain tumors.

Astrocytoma develops from a star shaped cell – the astrocyte, which supports the nervous cells in the brain. Astrocytoma are divided into four groups depending on the growth potential.

The most aggressive and fast-growing type is the grade 4 tumor, the glioblastoma multiforme (GBM).

Of all diagnosed astrocytomas around 80% belong to the GBM. The prognosis for the disease is very poor, and based on clinical data the 5-year survival is only 5%, making GBM the deadliest brain tumor in adults.

The mechanisms leading to GBM are still not fully understood, many patients with glioblastoma experience relapse, which frequently is accompanied by molecular alterations that have occurred after the initial diagnosis.

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Prognostic profiling of Glioblastoma

Gliomas are diffusely infiltrating tumors affecting the surrounding brain tissue.

Tumor classification based on gene expression profiles, genetic alterations, and DNA methylation changes have been intensively studied to provide an important prognostic tool to accompany the histopathological classification for the newly diagnosed glioblastoma patient.

Especially, as a consequence of the development and accessibility to high-throughput technologies as next generation sequencing, and comprehensive expression- and methylation arrays, the glioblastoma profiling is advancing fastly. Still, the picture is very complex, with a high number of molecular and epigenetic alterations affecting both tumor suppressor – and oncogenes (reviewed in Zhang et al. 2020)

One important prognostic classifier for GBM is the mutation status of isocitrate dehydrogenase (IDH).

IDH comprises a family of three genes: IDH1, IDH2 and IDH3, all associated with cancer. IDH1 is mainly cytoplasmic, and IDH2 and IDH3 are present in the mitochondrial matrix.

The enzyme IDH is a central part of the citric acid cycle, generating energy for the cell, and has a prominent role in oxidative stress resistance.

Mutations in IDH genes are frequently found in many different malignancies, including GBM and these prevent the cell from differentiating, and results in reprogramming of the cellular metabolism. GBM patients are divided into two groups associated with a prognostic and predictive status based on IDH mutation status. The IDH wild type (IDHwt) group has a poor prognosis, with additional mutations in tumor suppressor genes as: TP53, PTEN and CDKN2A, as well as in EGFR and the TERT promoter. The IDH mutated (IDHmut) group has in general higher overall survival than the IDHwt and are better responders to temozolomide (Han S et al. 2020).

IDH mutational status is associated with CpG island hypermethylation, and IDH1 mutation activity results not only in global DNA hypermethylation but also in histone methylation.

The IDH1 mutant converts alpha-ketogluterate into D-2-hydroxyglutarate, which acts as an inhibitor both for KDM4, involved in histone demethylation, and the TET protein, involved in demethylation of DNA.

The reversible nature of the DNA methylation process may be impaired in IDHmut cells and thereby contributing to the malignant transformation.

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MGMT Promoter Methylation

O6-methylguanine-DNA methyltransferase (MGMT) is a DNA repair gene, and a key player in chemoresistance to alkylating agents.

MGMT removes alkyl groups from the O6 position of guanine, which is an important target for DNA alkylation. Lesions induced by this chemotherapy, especially the O6-methylguanine triggers cytotoxicity and apoptosis of the cancer cell.

If MGMT is highly active, these lesions will be repaired, leaving the patients with minimal or no effect of the chemotherapy.

Epigenetic silencing by MGMT gene promoter methylation is associated with loss of MGMT function, thereby leading to inefficient repair of the alkylated DNA and increased effect of the alkylating chemotherapy.

Therefore, it is important to assess the MGMT promoter methylation status in newly diagnosed GBM patients before deciding, which line of therapy that would be of most benefit for the patient. (For further information, please visit the section: MGMT gene).

Even though silencing of the MGMT gene by promoter DNA methylation is considered a highly important prognostic and predictive marker for the outcome for glioblastoma patients, the implementation of this biomarker is still challenging.

Different technologies are used to assess the MGMT methylation status, and consensus has to reached as how to make clinical decisions based on the methylation status from the obtained results (reviewed in Mansouri A. et al. 2019).


How MethylDetect can assist your research in Glioblastoma

MethylDetect provides ready-to-use kits for DNA methylation analysis of your target of interest.

On you will find EpiMelt kits targeting a long range of genes, and most importantly for glioblastoma research the MGMT gene promoter (EpiMelt MGMT kit).

All EpiMelt kits contain a primer mix and a control set of 100% methylated, unmethylated, and an assay calibration control, to ensure the high sensitivity of your EpiMelt assays. Standard qPCR platforms with a high-resolution melting module can be used, please consult the protocol at, for further information on setting up the EpiMelt analysis in you laboratory.

If your target of interest is missing from our portfolio, we design and produce EpiMelt kits in collaboration with you, to ensure that the design fits your requirements for test material and expected methylation status (hypo- or hypermethylation). We design EpiMelt kits for DNA derived from sources as: FFPE tissue, liquid biopsies or high-quality DNA.

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Further Reading

Han S. et al. IDH mutation in glioma: molecular mechanisms and potential therapeutic targets. British Journal of Cancer (2020) 122:1580–1589.

Hegi ME et al. MGMT Gene Silencing and Benefit from Temozolomide in Glioblastoma. N Engl J Med 2005;352:997-1003.

Mansouri A et al. MGMT promoter methylation status testing to guide therapy for glioblastoma: refining the approach based on emerging evidence and current challenges. Neuro-Oncology 21(2), 167–178, 2019

Yu W et al. O6-Methylguanine-DNA Methyltransferase (MGMT): Challenges and New Opportunities in Glioma Chemotherapy. Front. Oncol., 17 January 2020

Zhang P et al. Current Opinion on Molecular Characterization for GBM Classification in Guiding Clinical Diagnosis, Prognosis, and Therapy. (2020). Front. Mol. Biosci. 7:562798.

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